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Search Results: 1 - 10 of 178339 matches for " Thomas H. Holmes "
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Habitat Associations of Juvenile Fish at Ningaloo Reef, Western Australia: The Importance of Coral and Algae
Shaun K. Wilson,Martial Depczynski,Rebecca Fisher,Thomas H. Holmes,Rebecca A. O'Leary,Paul Tinkler
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015185
Abstract: Habitat specificity plays a pivotal role in forming community patterns in coral reef fishes, yet considerable uncertainty remains as to the extent of this selectivity, particularly among newly settled recruits. Here we quantified habitat specificity of juvenile coral reef fish at three ecological levels; algal meadows vs. coral reefs, live vs. dead coral and among different coral morphologies. In total, 6979 individuals from 11 families and 56 species were censused along Ningaloo Reef, Western Australia. Juvenile fishes exhibited divergence in habitat use and specialization among species and at all study scales. Despite the close proximity of coral reef and algal meadows (10's of metres) 25 species were unique to coral reef habitats, and seven to algal meadows. Of the seven unique to algal meadows, several species are known to occupy coral reef habitat as adults, suggesting possible ontogenetic shifts in habitat use. Selectivity between live and dead coral was found to be species-specific. In particular, juvenile scarids were found predominantly on the skeletons of dead coral whereas many damsel and butterfly fishes were closely associated with live coral habitat. Among the coral dependent species, coral morphology played a key role in juvenile distribution. Corymbose corals supported a disproportionate number of coral species and individuals relative to their availability, whereas less complex shapes (i.e. massive & encrusting) were rarely used by juvenile fish. Habitat specialisation by juvenile species of ecological and fisheries importance, for a variety of habitat types, argues strongly for the careful conservation and management of multiple habitat types within marine parks, and indicates that the current emphasis on planning conservation using representative habitat areas is warranted. Furthermore, the close association of many juvenile fish with corals susceptible to climate change related disturbances suggests that identifying and protecting reefs resilient to this should be a conservation priority.
Speed calculations for random walks in degenerate random environments
Mark Holmes,Thomas S. Salisbury
Mathematics , 2013,
Abstract: We calculate explicit speeds for random walks in uniform degenerate random environments. For certain non-uniform random environments, we calculate speeds that are non-monotone.
Forward clusters for degenerate random environments
Mark Holmes,Thomas S. Salisbury
Mathematics , 2013,
Abstract: We consider connectivity properties and asymptotic slopes for certain random directed graphs on $Z^2$ in which the set of points $C_o$ that the origin connects to is always infinite. We obtain conditions under which the complement of $C_o$ has no infinite connected component. Applying these results to one of the most interesting such models leads to an improved lower bound for the critical occupation probability for oriented site percolation on the triangular lattice in 2 dimensions.
Random walks in degenerate random environments
Mark Holmes,Thomas S. Salisbury
Mathematics , 2011,
Abstract: We study the asymptotic behaviour of random walks in i.i.d. random environments on $\Z^d$. The environments need not be elliptic, so some steps may not be available to the random walker. We prove a monotonicity result for the velocity (when it exists) for any 2-valued environment, and show that this does not hold for 3-valued environments without additional assumptions. We give a proof of directional transience and the existence of positive speeds under strong, but non-trivial conditions on the distribution of the environment. Our results include generalisations (to the non-elliptic setting) of 0-1 laws for directional transience, and in 2-dimensions the existence of a deterministic limiting velocity.
A combinatorial result with applications to self-interacting random walks
Mark Holmes,Thomas S. Salisbury
Mathematics , 2011,
Abstract: We give a series of combinatorial results that can be obtained from any two collections (both indexed by $\Z\times \N$) of left and right pointing arrows that satisfy some natural relationship. When applied to certain self-interacting random walk couplings, these allow us to reprove some known transience and recurrence results for some simple models. We also obtain new results for one-dimensional multi-excited random walks and for random walks in random environments in all dimensions.
Degenerate random environments
Mark Holmes,Thomas S. Salisbury
Mathematics , 2011,
Abstract: We consider connectivity properties of certain i.i.d. random environments on $\Z^d$, where at each location some steps may not be available. Site percolation and oriented percolation can be viewed as special cases of the models we consider. In such models, one of the quantities most often studied is the (random) set of vertices that can be reached from the origin by following a connected path. More generally, for the models we consider, multiple different types of connectivity are of interest, including: the set of vertices that can be reached from the origin; the set of vertices from which the origin can be reached; the intersection of the two. As with percolation models, many of the models we consider admit, or are expected to admit phase transitions. Among the main results of the paper is a proof of the existence of phase transitions for some two-dimensional models that are non-monotone in their underlying parameter, and an improved bound on the critical value for oriented site percolation on the triangular lattice. The connectivity of the random directed graphs provides a foundation for understanding the asymptotic properties of random walks in these random environments, which we study in a second paper.
Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans
Christina Osborne,Paul M. Cryan,Thomas J. O'Shea,Lauren M. Oko,Christina Ndaluka,Charles H. Calisher,Andrew D. Berglund,Mead L. Klavetter,Richard A. Bowen,Kathryn V. Holmes,Samuel R. Dominguez
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019156
Abstract: Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.
Perceived Difficulty of Friendship Maintenance Online: Geographic Factors  [PDF]
Kristie Holmes
Advances in Applied Sociology (AASoci) , 2012, DOI: 10.4236/aasoci.2012.24040
Abstract: Geographic location has an effect on the perceived ease of friendship maintenance online and may reflect physical space. Participants from the Northeastern United States rated maintaining friendships online as more difficult than those from other regions. Those with the highest anxiety level ratings were from the largest and most densely populated areas (metropolitan) and those who were the least anxious about their image (both online and offline) were from rural areas with the least population density. Those residing in metropolitan areas were the most trusting of online information posted by others and the town/small city group were the least trusting of others’ online posted information (similar to the urban group), making those from rural areas nearly as trusting of others’ information as the metropolitan group, though probably the result of entirely different influences.
A Comparison of Statistics for Assessing Model Invariance in Latent Class Analysis  [PDF]
Holmes Finch
Open Journal of Statistics (OJS) , 2015, DOI: 10.4236/ojs.2015.53022
Abstract: Latent class analysis (LCA) is a widely used statistical technique for identifying subgroups in the population based upon multiple indicator variables. It has a number of advantages over other unsupervised grouping procedures such as cluster analysis, including stronger theoretical underpinnings, more clearly defined measures of model fit, and the ability to conduct confirmatory analyses. In addition, it is possible to ascertain whether an LCA solution is equally applicable to multiple known groups, using invariance assessment techniques. This study compared the effectiveness of multiple statistics for detecting group LCA invariance, including a chi-square difference test, a bootstrap likelihood ratio test, and several information indices. Results of the simulation study found that the bootstrap likelihood ratio test was the optimal invariance assessment statistic. In addition to the simulation, LCA group invariance assessment was demonstrated in an application with the Youth Risk Behavior Survey (YRBS). Implications of the simulation results for practice are discussed.
Advantages of Joint Modeling of Component HIV Risk Behaviors and Non-Response: Application to Randomized Trials in Cocaine-Dependent and Methamphetamine-Dependent Populations
Tyson H. Holmes,Shou-Hua Li
Frontiers in Psychiatry , 2011, DOI: 10.3389/fpsyt.2011.00041
Abstract: The HIV risk-taking behavior scale (HRBS) is an 11-item instrument designed to assess the risks of HIV infection due to self-reported injection-drug use and sexual behavior. A retrospective analysis was performed on HRBS data collected from approximately 1,000 participants pooled across seven clinical trials of pharmacotherapies for either the treatment of cocaine dependence or methamphetamine dependence. Analysis faced three important challenges. The sample contained a high proportion of missing assessments after randomization. Also, the HRBS scale consists of two distinct behavioral components which may or may not coincide in response patterns. In addition, distributions of responses on the subscales were highly concentrated at just a few values (e.g., 0, 6). To address these challenges, a single probit regression model was fit to three outcomes variables simultaneously – the two subscale totals plus an indicator variable for assessments not obtained (non-response). This joint-outcome regression model was able to identify that those who left assessment early had higher self-reported risk of injection-drug use and lower self-reported risky sexual behavior because the model was able to draw on information on associations among the three outcomes collectively. These findings were not identified in analyses performed on each outcome separately. No evidence for an effect of pharmacotherapies was observed, except to reduce missing assessments. Univariate-outcome modeling is not recommended for the HRBS.
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